deCoVar – the 𝐝𝐞𝐂𝐎DE 𝐯𝐚𝐫iant tools

An application with multiple sub-programs that perform useful transformations, filters, etc. on VCF/BCF files. Developed at deCODE genetics to fill-in gaps of bcftools.

Sub-programs

allele: reduce the size impact of multiallelic records by removing rare alleles and/or replacing the PL and AD fields with LPL and LAD (smaller, locally relevant fields).

Notable differences to BCFtools

No 2GB limit for records when reading/writing .vcf and .vcf.gz (we can do nothing about .bcf unfortunately).

Instructions

Getting it

We recommed using a package from the releases page.

Cloning and building from source *(click to expand)*

Please note that GCC>=10.3 is required; LLVM and MSVC are not supported.

Clone the latest main-branch:

cd ~/devel/                                                         # or some other directory
git clone --recurse-submodules https://github.com/h-2/decovar.git

Setup build folder:

mkdir -p ~/devel/decovar-build/release                              # or some other directory
cd ~/devel/decovar-build/release
cmake -DCMAKE_BUILD_TYPE=Release ../../decovar

Build:

make -j 4

Run:

./bin/decovar --help

Using

Look at the help-page for details:

path/to/decovar --help

Disclaimer

This is an early preview and everything is still subject to change.